<tool id="signac_add_gene_annotations" name="Add gene annotations" version="0.1.0" python_template_version="3.5">
<description> to your Signac object.</description>
<macros>
    <import>signac_macros.xml</import>
</macros>
<expand macro="requirements"/>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    Rscript '${__tool_directory__}'/signac-add_gene_annotations.R --signac-object $signac_object --ens-db-genome $ens_db_genome --annotations $annotations --output-object-file $rds_signac_seurat_file
]]></command>
<inputs>
    <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
    <param type="select" name="ens_db_genome" label="EnsDB genome version" multiple="false" format="text" optional="false">
        <option value="EnsDb.Hsapiens.v75">EnsDb.Hsapiens.v75</option>
        <option value="EnsDb.Mmusculus.v79">EnsDb.Mmusculus.v79</option>
    </param>
    <param type="select" name="annotations" label="" multiple="false" format="text" optional="false">
	<option value="GRCh38">GRCh38</option>
        <option value="hg19">hg19</option>
	<option value="mm10">mm10</option>
    </param>
</inputs>
<outputs>
    <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (genes annotated)"/>
</outputs>
<help><![CDATA[
This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
    ]]></help>
</tool>